Electron Cyclotron Resonance Ion Source (ECRIS) plasmas are prone to kinetic instabilities resulting in loss of electron and ion confinement. It is demonstrated that the biased disk of an ECRIS can be used as a probe to quantify such instability-induced electron and ion losses occurring in less than 10 µs. The qualitative interpretation of the data is supported by the measurement of the energy spread of the extracted ion beams implying a transient plasma potential >1.5 kV during the instability. A parametric study of the electron losses combined with electron tracking simulations allows for estimating the fraction of electrons expelled in each instability event to be on the order of 10% of the total electron population.